Analysis of the algorithm: From rankings to backup genes.
Ranking section
For each of the affected genes present in the list, a ranking with the score and percentile of every possible gene was obtained. Once this was done, the position for every known backup gene was obtained and the statistical descriptor of all the values calculated.
Table 1. Performance summary for every kernel and net before integration.
| Net | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| biological_process | ct | 1 | 1 | 1 | 1 | 0.958333333333333 |
| biological_process | el | 1 | 1 | 1 | 1 | 0.958333333333333 |
| biological_process | ka | 1 | 1 | 1 | 1 | 0.958333333333333 |
| biological_process | node2vec | 1 | 1 | 1 | 1 | 0.958333333333333 |
| biological_process | rf | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | ct | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | el | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | ka | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | node2vec | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | rf | 1 | 1 | 1 | 1 | 0.958333333333333 |
| genetic_interaction_weighted | ct | 1 | 1 | 1 | 1 | 0.96 |
| genetic_interaction_weighted | el | 1 | 1 | 0.666666666666667 | 1 | 0.96 |
| genetic_interaction_weighted | ka | 1 | 1 | 0.666666666666667 | 1 | 0.96 |
| genetic_interaction_weighted | node2vec | 1 | 1 | 1 | 1 | 0.96 |
| genetic_interaction_weighted | rf | 1 | 1 | 0.833333333333333 | 1 | 0.96 |
| molecular_function | ct | 1 | 1 | 0 | 1 | 0.923076923076923 |
| molecular_function | el | 1 | 1 | 0 | 1 | 0.923076923076923 |
| molecular_function | ka | 1 | 1 | 0 | 1 | 0.923076923076923 |
| molecular_function | node2vec | 1 | 1 | 0 | 1 | 0.923076923076923 |
| molecular_function | rf | 1 | 1 | 0 | 1 | 0.923076923076923 |
| pathway | ct | 0.551724137931034 | 1 | 0.333333333333333 | 1 | 0.918032786885246 |
| pathway | el | 0.482758620689655 | 1 | 0.166666666666667 | 1 | 0.935483870967742 |
| pathway | ka | 1 | 1 | 1 | 1 | 0.90625 |
| pathway | node2vec | 1 | 1 | 0.5 | 1 | 0.90625 |
| pathway | rf | 0.448275862068966 | 1 | 0.166666666666667 | 1 | 0.935483870967742 |
| phenotype | ct | 1 | 1 | 0 | 1 | 0.956521739130435 |
| phenotype | el | 1 | 1 | 0 | 1 | 0.956521739130435 |
| phenotype | ka | 1 | 1 | 1 | 1 | 0.956521739130435 |
| phenotype | node2vec | 1 | 1 | 1 | 1 | 0.956521739130435 |
| phenotype | rf | 1 | 1 | 0 | 1 | 0.956521739130435 |
| protein_interaction | ct | 0.902430555555556 | 1 | 0.166666666666667 | 1 | 0.972602739726027 |
| protein_interaction | el | 0.861111111111111 | 1 | 0.166666666666667 | 1 | 0.972602739726027 |
| protein_interaction | ka | 1 | 1 | 0.833333333333333 | 1 | 0.96 |
| protein_interaction | rf | 0.902777777777778 | 1 | 0.166666666666667 | 1 | 0.972602739726027 |
Table 2. Performance summary for every kernel after integration
| Integration | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| integration_mean_by_presence | ct | 1 | 1 | 0.666666666666667 | 1 | 0.96 |
| integration_mean_by_presence | el | 1 | 1 | 0.333333333333333 | 1 | 0.96 |
| integration_mean_by_presence | ka | 1 | 1 | 0.5 | 1 | 0.96 |
| integration_mean_by_presence | node2vec | 1 | 1 | 1 | 1 | 0.96 |
| integration_mean_by_presence | rf | 0.625 | 1 | 0.5 | 1 | 0.966442953020134 |
| mean | ct | 1 | 1 | 0.666666666666667 | 1 | 0.96 |
| mean | el | 1 | 1 | 1 | 1 | 0.96 |
| mean | ka | 0.736111111111111 | 1 | 0.333333333333333 | 1 | 0.965986394557823 |
| mean | node2vec | 1 | 1 | 1 | 1 | 0.96 |
| mean | rf | 1 | 1 | 1 | 1 | 0.96 |
Backup Pairs Coverage By Layer
Backup Pairs Coverage By Layer
Backup Pairs Coverage By Layer
Backup Pairs Coverage By Layer
Backup Pairs Coverage By Layer
CDF plots of non integrated kernels
ROC plots of integrated kernels
ROC plots of integrated kernels
CDF plots of integrated kernels